Using differential display we have identified a differentially expressed gene obtained from the substantia nigra of a Parkinson brain. Total RNA was isolated from microdissected human brain substantia nigra compacta. The gene that was upregulated is flotillin-1. We have focused our attention on this novel gene which is implicated in the formation of caveolae within vesicular organelles. We have also discovered a deletion mutation of flotillin from the substantia nigra compacta of a Parkinson brain. We compared age matched Parkinson and normal brains for flotillin mRNA in the substantia nigra using in situ hybridization histochemistry. It was observed that the density of flotillin was reduced in Parkinson brains. With the in situ hybridization histochemical method we demonstrated the presence of flotillin in mRNA in the substantia nigra of the human brain. In addition, flotillin was observed in the cells of the dorsal raphe, nucleus of the third nerve (n.III N), nucleus of the fourth nerve (n.IV N), locust coeruleus, pontine nucleus and cerebral cortex. In the rat and mouse brains flotillin mRNA was observed in the hypoglossal nucleus (n.XII N), vagus nucleus (n.X N) and facial nucleus (n.VII N).